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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

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Updated: May 25, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

BIGpre: a quality assessment package for next-generation sequencing data.

Tongwu Zhang1, Yingfeng Luo, Kan Liu

  • 1CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China.

Genomics, Proteomics & Bioinformatics
|February 1, 2012
PubMed
Summary
This summary is machine-generated.

BIGpre is a new, user-friendly software for assessing next-generation sequencing (NGS) data quality. It effectively handles duplicate reads, considering sequencing errors, and is available for Illumina and 454 platforms.

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Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Next-generation sequencing (NGS) offers high throughput but generates complex data with challenges like short reads and duplicates.
  • Existing NGS data quality assessment tools are often inaccessible or lack comprehensive error handling for duplicates.
  • Sequencing errors complicate duplicate read assessment in current NGS quality control software.

Purpose of the Study:

  • To introduce BIGpre, a user-friendly software package for comprehensive quality assessment of NGS data.
  • To address limitations in existing tools by incorporating error-aware duplicate read detection and low-quality read trimming.
  • To provide a versatile solution for both Illumina and 454 sequencing platforms.

Main Methods:

  • BIGpre is developed using Perl and integrates R for graphical output.
  • The software performs quality assessment tasks including read correlation, GC-content distribution, and base quality analysis.
  • It includes novel functionalities for detecting and removing duplicate reads while accounting for sequencing errors and trimming low-quality reads.

Main Results:

  • BIGpre provides both tabular and graphical summaries of sequencing data quality.
  • The software efficiently processes millions of reads within minutes, offering rapid diagnostic information.
  • It successfully integrates standard quality assessment functions with advanced duplicate handling.

Conclusions:

  • BIGpre offers a user-friendly and comprehensive solution for NGS data quality assessment.
  • The software's ability to handle sequencing errors in duplicate detection enhances data reliability.
  • BIGpre is freely available and facilitates efficient downstream analysis for Illumina and 454 sequencing data.